Mysterious Eyes
by Scribe of Turesa
Summary: She showed up...and things just kept changing. When a young mutant shows up and the guys are left with a huge task what will happen when more mutants start showing up? What happens when the worst looks like it could be coming...
1. Chapter 1:Arrival of Grace

**Disclaimer: ****Still no...except the OCs you will soon see…**

**Chapter 1: Arrival of Grace**

She was running, frantically trying to get away from her pursuers. She stumbled and cried out as the figure she had been cradling crumpled to the ground. The figure in her arms cried out, sobbing a little Teripan girl peeked out of the cloak she had been wrapped in.

"MAMA!" The girl sobbed as her mother struggled to sit up.

~*~

"Yes Leo, we've got the hover car ready, yeah, yeah we're comin'," Raph grumbled into the phone.

Don gave Raph a "really?" look to which he received a dirty look. Raph muttered something as he clicked the phone shut.

"Naggin'," Raph grouched.

Don chuckled.

"He's only worried you know," Don sighed as he straightened before observing the supplies attached to the hover car.

Raph snorted before climbing up and getting in front of the steering wheel.

"Yeah waheva," Raph grumped.

"Ever since you pulled the whole Nightwatcher gig he worries that you'll go lone wolf again," Don chuckled as he came and sat down.

"That was three years ago," Raph commented, "we're a team again…I've got the sore muscles to prove it."

"Still sore from practice Raphie?" Don teased.

"Shud'up," Raph growled, though a hint of a smile turned up his mouth.

Don chuckled before checking the straps behind them once more and nodding for Raph to go.

The hover car hummed to life as it lifted up of the ground and shot down the main line. Don's head jerked around when they past a boarded up area and he heard a wail.

"RAPH STOP!" Don shouted.

Raph jumped and slammed the Hovercar into park, it settled down with a groan onto the water.

Don jumped out and shot toward the area.

"What the-Don!" Raph growled, jumping out after Don's sprinting form.

Don rounded the corner first and came to a halt, brown eyes widening in shock.

Raph nearly ran him over.

"What the Donnie-Whoah," Raph gasped, "she's…a….a-"

"Turtle," Don finished.

She was sprawled on the ground, black hair spread around her, pale-green-white skin was stained with splattered red. Her plastron was white as was her carapace. A loose cloak hid half of her frame and a leather skirt hid her lower body.

They jumped when a whimper caught their attention. Crouched next to the female turtle was a younger turtle, a little girl, with the same dark hair, but her complexion was slightly darker. She was clutching what looked like a ragged teddy-bear and wearing a simple leather dress. Large, shocked, golden-brown eyes stared back at them.

"She's got a kid," Raph gasped.

Don seemed to snap out of his reverie and moved forward, carefully kneeling down and checking the female's pulse.

"Raph run back to the hover car and get the medical supplies now! Call Leo and tell him we need the infirmary ready!" Don ordered as he carefully rolled the young woman onto her carapace and started CPR.

"STOP HURTING MY MOMMY!" the girl wailed, latching onto Don and trying to push him away.

Don turned to the girl and gently pulled her into a hug.

"Shhhh…I'm trying to help her," Don coaxed.

"She…won't wake up," the toddler whimpered after she realized that Don was a friend.

"I'll be ok," Don coaxed, "shhh."

Raph came rushing back and found himself doing CPR as Don attempted to calm the sobbing toddler.

~*~

Don rushed into the lair with Raph cradling the woman in his arms. Don had the girl on his back and was frantically attempting to stay calm, if for no other reason than to keep the girl relaxed.

"Don what did Raph-wait….where did you-?" Leo started as he spotted the young woman.

"Sewers, is the infirmary ready?" Don asked.

Leo nodded and stepped back as Raph rushed past. Leo's eyes widened when he saw the woman.

"No…" Leo breathed, "it can't be…"

No one noticed what he had said, much to his relief. Mike came out and received the crying girl and was ordered to entertain her. Leo remained frozen, eyes flicking from the young woman to the girl. His golden-brown eyes widened as spotted the woven leather necklace with a white and blue carved stone rose.

"Grace…" Leo gasped as he turned back toward the infirmary.

It was all he could do not to sprint toward it, they couldn't know, not yet. But never the less he moved quickly trying to help best he could.

~*~

April had just arrived when Don came out, he looked shaken, deeply sad, and a little lost.

Leo looked at him, afraid to ask, they couldn't know.

"Donnie? I brought those things," April said softly.

"Where's the little girl?" Don mumbled.

"Asleep, Mikey convinced her to curl up over there," Raph whispered, gesturing toward the couch.

Don simply nodded before looking at April.

"She won't need all that…I…I couldn't save her," Don mumbled.

Leo closed his eyes and fought the wave of grief that hit him, they couldn't know.

"Do you know ht child name, the young woman's?" Master Splinter murmured.

"Her name was Grace…….and her daughter's name is…Amber…" Don replied, "she asked me to find the girl's father…but she didn't give me the name…."

Leo bowed his head and gave the girl, his _daughter_, on the couch a sad look.

"Very well…we will bury her up at the farmhouse…I am sure Mr. Jones will not protest," Master Splinter murmured, glancing toward the man that had just recently arrived.

Casey nodded in affirmation.

A silence settled over the group as the infirmary was closed off. After the others had all wandered off Leo slipped into the infirmary and stood over the covered body. He pulled back the sheet, pressed a kiss to Grace's forehead, let a few tears fall and covered her back up.

"I'll take good care of her…I'm sorry I never came back," Leo murmured.

He sat and simply wept softly, forcing his tears to silence as he grieved best he could without alerting the others to where he was.

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Ok everyone…I've long been debating on whether or not to do this one…but…I've chosen to…please review for me!!


	2. Chapter 2:Lullaby

***I own **_**The Rain Dream Lullaby.**_

**Chapter 2: Lullaby**

It had been three weeks since the guys had buried Grace, the mysterious female turtle that was so wrapped in confusion. Little Amber was utterly lost and confused, clutching the doll that her mother had made for her and whimpering as she softly called out for Grace. None of the guys seemed truly able to handle the confused grief the child possessed. Not even Mikey could get the girl to smile.

"I give up," Mikey moaned as he sat down in the chair within the kitchen at the farmhouse.

April gave him a sad look.

"She's grieving Mikey, she's just a kid, though more confused than sad I think," April sighed.

April pressed a hand to Mike's shoulder and offered a gentle smile.

"Yeah I know but I mean, I've always been able to make kids laugh ya' know?" Mikey sighed.

"I don't think that kid will ever smile Mike" Raph grumbled as he came in and opened the fridge, "and who knows when those nightmares of her's will end."

"Most likely after she settles into a new pattern…a new family mold. I'm still struggling to figure out how I'm-we're supposed to find this father," Don sighed, sitting next to Mikey.

"Sensei says we're supposed to find him but like…he could be anywhere!" Mikey moaned.

April sighed as Casey joined them.

"Master Splinter is meditating and Leo's off for a walk again," Casey commented.

"Again?" Raph gasped, "he's been all weird since that Grace died and the kid showed up."

"You don't think…" Casey trailed off, eyes widening at the thought.

The whole room froze at the contemplation of what had been offered.

"Nahhhh," they all said together.

"Where's Amber?" April said suddenly.

"Down for a nap," Don said quickly.

April relaxed and then jumped as scared screams alerted them that Amber was having another nightmare. Everyone started to get up at once.

They all froze as they heard a rich baritone begin singing.

"_Hush…hush little star…drip drop….let thy eyes close….drip drop….hush little flower in my arms…drip drop…water touches lilies and says….hush sweet little angel, let thy eyes close…let dreams take you on wings of gold as the world slows…let thy eyes close…little angel…little angel…close thy eyes and dream…dreams…dreams that sing of stars across the heavens of laughter in the sun…hush little angel and dream…drip drop…hush little angel and sleep…sleep and dream…of me…"_

"Was that-" Don gasped.

"Leo?" April finished.

"Yeah," Mikey managed after a minute.

Raph stared down the hall in stunned amazement.

A soft clearing of the throat made them turn, Master Splinter was standing in the doorway.

"Leonardo wishes to speak to us as soon as the girl is fast asleep," Master Splinter whispered.

"No way," Don gasped, "is _he_-?"

"All will be explained later" Master Splinter interrupted gently.

~*~

They were seated in the living room when Leo came in, he was wearing a loose woven cloak that April remembered instantly, the cloak he had often been seen in in Latin America.

"That's the-" she started.

"Cloak that the Ghost of the Jungle was seen in," Leo cut off, smiling a little.

He knelt in front of them and took a deep breath. They all glanced at each other and sifted nervously.

"I am Amber's father…I met Grace five years ago…not long after I arrived in Latin America for my training. We were shocked to have found someone like ourselves but did not think much of each other beyond idle curiosity," Leo started.

Raph snorted a little to which both Leo and Master Splinter shot him look. Mikey sniggered a little.

"I wasn't until I was wounded by poachers that we really spoke to each other in great length…I had been shot in the chest and if she had not been where she was I wouldn't be here today. It was the worst four months of my life. I could barely breath and constant, unrelenting pain was my companion. When I finally woke…she was tending me. After I had gained my strength I went back to my training, but I always came back to her at night…rested in the cave she had…shared the food we gathered…slowly I began to care for her…as the second year dawned…something none of you have ever endured met me…she went into heat and…" Leo trailed off blushing slightly.

April blushed.

"I went into rut not long after…we separated…attempting to prevent a child neither of us were ready for…after two months we were able to again be within ten feet of each other…six months later Jefe arrived in the village she protected…she was shot…I barely avoided a bullet to the head as I defended her…I had forgotten that she had been hinting…hinting that she was going into heat again…I stayed with her to tend her injury…three weeks later Grace told me the news…then vanished…she…left a note…said she had to find an old friend…that she'd be back."

Leo sat still and hunched there. April started to move forward but Leo looked up at them again.

"Jefe had been looking for us though…he found the cave when I was asleep one night…set the area on fire I had no way out…I found out too late that she had returned in the night and was curled beside me…in our attempt to escape the flames…we were separated again…I killed Jefe not long after, him, and his men…three weeks later April came and told me that you all needed me back home…I…I looked everywhere for her…four days I wavered and then went back to the cave…she was there, grieving…she thought I was dead…I swore to her I'd be back in time…I broke that promise…" Leo trailed off as tears started and he put a hand over his mouth.

April moved faster than the eye could follow and wrapped him in a hug. Cradling him as sobs broke forth.

"Shhh…oh Leo," April whispered gently.

"I broke my oath," Leo sobbed.

Master Splinter stood and gently pressed a hand to Leo's carapace.

"Oh my son," Master Splinter whispered soothingly.

None of his brothers moved, too shocked too both by the story and the sight of Leo weeping.

But Mikey got up after a minute and wrapped Leo up, tightening the hug so Leo could lean against him. Two other sets of arms wrapped around him a few seconds later and Casey laid a hand on Leo's shoulder, gently comforting the heartbroken figure.

They stayed like that for a while as Leo allowed himself to grieve for Grace. Then Leo straightened and bowed completely over in front of Master Splinter.

"Sensei I ask your forgiveness for my-" Leo started.

"Leonardo, I will not punish you for this…three years of the burden you have carried is enough punishment…tend to your daughter, help her accept her new life with this family," Master Splinter interrupted gently.

Leo sat up and wiped his tears away.

"Thank-you Sensei," he murmured.

"She's crying again," Mikey mumbled, glancing down the hall.

Leo got up and moved that way casting his family a thankful look as he left.

"Great," Raph sighed, "I hate kids."

Don snorted and rolled his eyes.

"I don't know how I didn't see it honestly…she looks a lot like him…" Don muttered, "and Raphie quit acting all tough…you've tried to comfort her as much as we have…"

Raph rolled his eyes and grumbled.

"Well…I have feeling thigns are going to become very different around the lair huh?" April teased.

"Oh man…this means no more scary movies and…and…." Mikey started, blue eyes widening in horror.

The other laughed softly.

~*~

Amber whimpered in her sleep, started to cry and then quieted as Leo lifted her and hugged her tight, singing softly.

"Hush little angel," Leo coaxed as the girl snuggled against him, her dark hair falling over his arms as she wrapped her little arms around his neck and clung to him.

"Daddy," she mumbled.

Leo blinked and then let a single tear fall before kissing her forehead.

"Yes…I'm your daddy," Leo whispered.

* * *

Reviews Please!!


	3. Chapter 3:Learning to Cope

**Chapter 3: Learning to Cope**

The others were sitting at the table in the living room when Leo returned, all but Don who had gone to get something. Leo walked in, his cloak left with Amber.

Leo paused as they glanced up at him.

"Why didn't you tell us before?" Mikey asked softly.

"I…I was scared of what you would all think…" Leo whispered, "what you would say…I was afraid of being…chased out I guess…"

Leo shrugged as he sat down, head resting in his hands.

Master Splinter gently placed a hand on Leo's shoulder.

"My son…we are your family…we would never do such a thing. I am deeply saddened to hear that you were not able to be there for your daughter's birth. I am not disappointed my son, but deeply sad that you feared such retribution from us that you never told us before…let your heart grieve for Grace, we will always be by your side," Master Splinter whispered.

Leo nodded, body hunched, they could hear him sniffing.

Don came back in, cradling a leather-bound package.

"Leo…she wanted me to…give this to you," Don whispered as he gently put the package in front of his brother.

Leo looked up at it and gently touched it, before slowly untying the leather and letting it fall open.

A letter sat atop two necklaces and a leather journal.

Leo touched the journal.

"Her…journal…" Leo breathed, before gently touching the letter and the two necklaces.

He lifted one gingerly; it was woven leather with a white and clear carved rose at the center and white stone vines leaping away from it.

"She always wore this…" Leo whispered, "it was her favorite flower…"

Then his eyes fell onto the other necklace and he tensed before touching it. It was metal, harsh, cold, metal, with dog tags hanging from it. When he tipped it up he shook his head in confusion.

_ID : 89_

_Gender: Female_

_Race: Testudines sapien_

_Name ID: Graceful Hunter_

_Current Age: 18_

_Offspring: 1(female)_

_Number of Missions Completed: 20_

_Team Members: 72, 45, 19, 22, 96, and 033._

_Rank: Kunochi _

_Skills: Seduction, murder, espionage, dance, art, song, traps, and strategy._

_Weight: approximately 150 lbs._

_Height: 5'_

Leo remained motionless, confusion and pain etched into his features, he dropped the dog tags and sat back, hands curling into fists as he struggled for breath.

"Leo?" Don whispered.

"She tricked me," Leo choked out, before glaring at the journal and the letter.

He reached forward and snatched it up hand clenched around it as he fought against the rage and the pain that writhed inside him.

Raph picked up the dog tags and gasped after skimming them.

"Leo…I'm sorry bro," Raph murmured.

Don and Mikey gave Leo pitying looks.

Leo stood up, and ripped open the letter, eyes skimming the page. As he read it he relaxed and sank into the chair the letter falling to the floor as he finished.

_Leo,_

_I ask that if there is anyway for you to, please forgive me. Please read my journal and…remember…that in the end…I did love you. I really did. Protect our daughter, your family. Don't trust the others and whatever you do…don't trust Jacob Lionel. Please Leo…help me protect what I realized was right in the end. Don't let them out of your sight…they'll be looking for me and Amber…be careful…I love you._

_-Graceful Hope._

"My son?" Master Splinter coaxed, gently pressing a hand to Leo's shoulder.

"No one leaves this house tonight," Leo ordered, his voice thick with emotion.

The others nodded a little, unsure why but they would trust Leo, they always had.

~*~

They stepped up to the edge of the woods beyond the barn, golden eyes glittering as they observed the figures inside.

"Des?" A whisper asked, a young turtle showed herself, slender, agile and beautiful.

The one in question turned her frame showing her reptilian figure, the long cream colored tail, a lizard, her clawed hands were twitching at her sides.

"It's him…Leonardo…she lead us to him anyway. Minx!" The female lizard hissed.

A black vixen stepped out of the shadows, her golden eyes glittering as they met the Lacertilia in front of her.

"Yes?" she whispered.

"Take your team and complete your mission…we have found our prey," the lizard hissed, her golden eyes flashing in delight.

The vixen bowed and the shot off, four others chasing after her, their figures just visible in the shadows, all of them furred..

"Nefertiti?" the lizard hissed as a faint rustling met their ears.

She and the other two, both turtles, turned. Seconds later a large Egyptian Cobra reared above them, fierce garnet eyes blazing against the pale tan-cream face, a darker hood flared open, pale underneath, accenting her throat and slender figure.

"My lady…Grasssse is gone…ssssshe is buried beyond the barn," Nefertiti hissed.

"Very well," the lizard murmured.

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	4. Chapter 4: Grace's Journal and Whispers

**Chapter 4: Grace's Journal and Whispers**

_I'm fourteen and I've finally been allowed to see the others like me, my training so far has been nothing but intense strict exercise, now, I get a team to work with…_

Raph flicked the lights on in the living room causing Leo to jerk awake on the couch, nearly sending his daughter flying in the process.

"Shell Raph what the-?" Leo growled, rubbing his eyes.

"Daddy?" Amber whimpered as she rubbed her eyes.

"Aww shell sorry bro," Raph whispered as he knelt and picked up the journal that Leo had knocked to the floor.

"Go back to sleep sweetheart," Leo coaxed as his daughter snuggled back against him.

As she drifted back off with "mae", her doll, hugged tightly, Leo looked at Raph.

"I'm sorry I didn-" Raph started as he handed the journal to his brother.

"It's ok, I fell asleep should have gone to bed anyway. What time is it?" Lo asked as he found his spot in the journal and marked it before setting it aside.

Raph glanced toward the clock.

"Um…around like six in the morning," Raph sighed, "You've been reading that for _days_ bro. Have you found anything out?"

"A lot…" Leo mumbled, eyes misting over as he gently stroked his daughter's hair, "this Jacob Lionel…he…he's been collecting mutants…training them to find more and…Grace was trained for that…she was just a kid when she was tricked into making a mutant child follow her…he was killed and she…she was rewarded."

Raph shuttered.

"But…you? Why didn't she just kill you?" Raph murmured.

"I haven't gotten that far yet…her hand writing is kinda confusing sometimes…" Leo mumbled.

Raph grabbed a chair and sat next to Leo, head resting on the back, amber eyes watching his niece sleep.

"She's beautiful you know that bro?" Raph murmured suddenly, "and she's got your…how do you say it? Your drive I guess."

Leo smiled and glanced at his daughter.

"She's got her mother's personality though…real quiet…at least…that's the Grace I knew anyway…" Leo mumbled.

"Go get some rest bro," Raph coaxed, "let the journal be for a while."

Leo shook his head.

"I can't…she was trying to warn me about something…I have to figure out what…" Leo sighed, rubbing his temples in frustration.

"Being exhausted won't help though," Raph pointed out.

Leo shot him a slightly annoyed look but smiled a little.

"Yeah…since when did you become all mellow?" Leo teased softly.

"I became an Uncle and inherited a mess…you've been running yourself ragged so much that Splinter put me in charge of training until you figure out what you're looking for in there," Raph chuckled, gesturing to the journal.

Leo nodded and sighed.

"Thanks…" he managed.

"Eh…no prob bro," Raph said simply, watching as Leo picked up Amber and headed for the stairs.

"He better get some sleep," Raph mumbled before walking into the kitchen and freezing as he thought he saw something in the window.

"What the hell?" he whispered before fumbling with his Sais and moving toward the back door.

~*~

Leo laid Amber down and covered her up, gently pressing a kiss to her forehead. He walked out into the hall and closed the door, taking a double take for a second at the window. He blinked and shook his head.

"I really need some sleep…" he mumbled, "seeing things…"

~*~

Raph stepped out onto the back porch and looked around, he froze when creaking above him alerted him to the fact that he wasn't alone.

"Ssssssssssssssssssssssss," rippled through the air.

Raph whipped around, Sais poised for an attack. There was nothing behind him.

"WHOSE THERE?" he shouted as another hiss made him turn.

"," a soft hiss murmured as Nefertiti coiled behind Raph.

Raph turned slowly, just catching a glimpse of the gold and black stripped scales of the cobra behind him.

"What the?" he started as he turned.

"HEY!" a shout called.

Nefertiti hissed in rage and vanished onto the other side of the porch, the shadows swallowing her up.

Her garnet eyes glittered angrily before winking out.

Raph turned to find Don standing in the doorway looking scared.

"Raph? What was that noise?" Don managed.

"I-I'm not sure bro…" Raph managed before grabbing Don and dragging him back inside and locking the door.

"Raphie?" Mikey asked as he came in to find Raph leaning against the counter, limps shaking.

Don pressed a hand to Raph's carapace.

"Raph?" Don coaxed gently.

"It was…hunting me…" he managed finally.

"What?" Don asked, a look of confusion rippling over his features.

"The other mutant," Leo whispered as he joined them in time to hear the conversation.

Raph looked up and nodded.

"I think it was…a…a snake…" he managed, "it was huge…"

Leo tensed and turned toward the closed journal, he walked over and picked it up before flipping it open.

"Get the others…Mikey bring Amber down here…" Leo ordered.

Don shot off to wake everyone and Mikey dashed upstairs toward his niece.

_There are ten of us here. All but one are female. Nefertiti named after the Egyptian Queen who she was thought to be by the natives, Abu a King Cobra, the only male among us, Minx, a silver fox vixen, Sedona, one of the three turtles, Emer, another turtle, Desiree, a lizard as ruthless as they come, named for her flirtation and in French since they found her in France, Sarah, a raccoon, Luna, a skunk with marvelous markings, Amadahy, a river otter, and me…Graceful Hunter the third turtle…_

"Shell," Raph managed nervously.

"We must leave this place…find shelter elsewhere…they seem to have been trying to approach at night…we need to leave now," Master Splinter said firmly.

A soft creaking in the kitchen made them stand. April tensed, gripping Amber who was sitting in her lap.

Casey slowly picked up a baseball bat that had been beside him.

"Hello," a whisper called, "we're here…"

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Reviews PLEASE!

"sniggers" ok sorry for the cliffy! Artwork for the OCs will be up on Deviantart soon, I have a few up already! Take a look and tell me what you all think!!


	5. Chapter 5:Glitterings

**Sorry for the delay guys I haven't had two seconds to myself lately…ugh…life just got in the way.**

**Onward!**

**Chapter 5: Glitterings**

"_We're here…"_

Amber, awake now, squirmed out of April's grip and rushed to Leo, hugging one of his legs and whimpering.

"Daddy," she whispered.

Leo rested a hand on her carapace as he eyed the kitchen area.

Amber pulled on Leo's belt.

"Daddy I'm scared hold me," she whimpered.

Leo grabbed her and cradled her on his hip with one hand reaching toward the hilt above his left shoulder.

Amber buried her face against his plastron and hugged his neck.

Soft creaking alerted them to the movement of those in the kitchen.

Raph stepped forward and half shielded Leo and Amber, giving the girl some cover…

*****

Sorry guys I've lost the muse and my notes for this. If I ever get them back I will finish this story.

Sorry.

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Reviews Please.


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